2003 Chrysler Town and Country Coil, plugs, wires, computer

Our van started running rough, we took it to a certified mechanic, who diagnosed the problem as a bad coil. They said the coild going bad fried the wires, and fouled the plugs. They replaced the coil, plugs, and wires. Then they said that this spiked the cars computer? They tried downloading software provided by the dealership, but this has not worked, and are now waiting for ne sofware to "re-boot" the computer. They stated if this doesn't work they will have to replace the ccars computer?

Any comments and or suggestions, they have had the car for 6 days now?